Comment on "Widespread RNA and DNA sequence differences in the human transcriptome"

Li et al. (Research Articles, 1 July 2011, p. 53; published online 19 May 2011) reported large numbers of differences between DNA and messenger RNA in human cells, indicating unprecedented levels of RNA editing, and including sequence changes not produced by any of the known RNA editing mechanisms. However, common sources of systematic errors in high-throughput sequencing technology, which were not properly accounted for in this study, explain most of the claimed differences.     

Different B cell populations mediate early and late memory during an endogenous immune response

Memory B cells formed in response to microbial antigens provide immunity to later infections; however, the inability to detect rare endogenous antigen-specific cells limits current understanding of this process. Using an antigen-based technique to enrich these cells, we found that immunization with a model protein generated B memory cells that expressed isotype-switched immunoglobulins (swIg) or retained IgM. The more numerous IgM(+) cells were longer lived than the swIg(+) cells. However, swIg(+) memory cells dominated the secondary response because of the capacity to become activated in the presence of neutralizing serum immunoglobulin. Thus, we propose that memory relies on swIg(+) cells until they disappear and serum immunoglobulin falls to a low level, in which case memory resides with durable IgM(+) reserves.     

Species compositional similarity and ecoregions: Do ecoregion boundaries represent zones of high species turnover?

The concept of an ecoregion, a discrete spatial area where species composition is presumed to be relatively homogeneous compared to that between areas, has become an increasingly common conservation tool. We test the effectiveness of one ecoregion delineation (World Wildlife Fund) in capturing patterns of change in species composition of birds, mammals, and trees across the United States (excluding Hawaii) and Canada, and describe the extent to which each ecoregion boundary is concurrent with relatively large changes in species composition. Digitized range maps were used to record presence/absence in 50 × 50 km equal-area grid cells covering the study area. Jaccard’s index of similarity was calculated for all pairs of cells in the same or adjacent ecoregions. The average rate at which similarity declined with geographic distance was calculated using pairs of cells within the same ecoregion (intra-ecoregion turnover) or using pairs of cells in adjacent ecoregions (inter-ecoregion turnover). The intra-ecoregion rate varies widely among ecoregions and between taxa, with trees having a faster rate of similarity decline than mammals or birds. For all three species groups, most ecoregion boundaries have similar rates across them (inter-ecoregion) than that within each adjacent ecoregion (intra-ecoregion), with the exception of zones of transition between biomes and major geographical features. Although the ecoregion concept is useful for many other conservation applications, the lack of systematic, high turnover rates along ecoregion boundaries suggests that ecoregions should not be used as a quantitative basis for delineating geographic areas of a particular taxonomic group.     

Effect of dextransucrase cellobiose acceptor products on the growth of human gut bacteria

The selective fermentation by human gut bacteria of gluco-oligosaccharides obtained from the reaction between the glucosyl group of sucrose and cellobiose, catalyzed by dextransucrases (DSR) from Leuconostoc mesenteroides , has been evaluated. Oligosaccharides were fractionated according to their molecular weight, and their effect on the growth of different bacterial groups was studied. To determine the structure (position and configuration of glycosidic linkages)-function relationship, their properties were compared to those of DSR maltose acceptor products (DSRMal) and of recognized prebiotic carbohydrates (fructo-oligosaccharides, FOS). Cellobiose acceptor products (DSRCel) showed bifidogenic properties similar to those of FOS. However, no significant differences related to molecular weight or isomeric configurations were found for DSRCel and DSRMal products.     

Evaluation of the visual stress grading standard on French Spruce (Picea excelsa) and Douglas-fir (Pseudotsuga menziesii) sawn timber

? In this paper an evaluation of the visual grading standard for softwood sawn timber was made.

? In order to do so, visual grading according to EN 518 and theoretical grading according to EN 338 and EN 384 (measurements of MOE, MOR and density) were applied to lumber. Two batches of 111 and 102 French boards were graded, respectively, of Spruce (Picea excelsa) and Douglas-fir (Pseudotsuga menziesii). For the visual grading the most discriminant criterion was noted: knots, cracks, wane, etc.

? Finally, the results of the two grading methods were compared, and it was shown that the visual stress grading gave quite low results for our two French species.

     

Surface-water gley soils in Bangladesh: Genesis

Extensive areas of periodically wet, acid soils in Bangladesh have a seasonally fluctuating pH of the surface horizon and evidence for net clay loss. Morphological, chemical, mineralogical and other data mainly on a typical profile of these surface-water gley soils indicate a clay loss of some 1.5 kg/dm' ; alteration of smectite to a soil chlorite, interlayered material with trapped ferrous iron; the consequent drop in C.E.C. of the clay fraction; and the presence of amorphous silica. The data were used to reconstruct a sequence of three soil forming processes: Vertisol formation, then argilluviation, followed by ferrolysis.Ferrolysis involves, in the wet season: reduction producing ferrous iron, which displaces part of the exchangeable basic cations and aluminium; leaching of bases and part of the aluminium; and interlayer formation by the remaining aluminium while some exchangeable ferrous iron is trapped in the interlayers. In the dry season, oxidation of exchangeable ferrous iron produces exchangeable hydrogen, part of which attacks the clay minerals and is neutralized by liberation of Al, Mg and other ions from the clay structure. Part of the silica remaining from the clay structure is leached out in the next wet season, part accumulates in amorphous form. In soils long used for paddy cultivation, man has concentrated the ferrolysis process in the ploughed layer by the formation of a slowly permeable ploughpan causing strong reduction only in the surface horizon.The hydromorphic albic horizon over more clayey material is indicative of the dominant process in surface-water gley soils. This sequum could usefully have a more important place in soil classification than it has at present, e.g. at great group level.     

COMPUTED TOMOGRAPHIC AND RADIOGRAPHIC CHARACTERISTICS OF AORTIC LESIONS IN 42 DOGS WITH SPIROCERCOSIS

Spirocerca lupi is a common cause of vomiting, regurgitation, and sudden death in dogs that live in tropical or subtropical regions. Sudden death due to aortic rupture may occur with no preceding clinical signs. The purpose of this prospective study was to compare radiographic and computed tomographic (CT) characteristics of aortic lesions in a cohort of 42 dogs with endoscopically confirmed spirocercosis. Dorsoventral and right lateral recumbent thoracic radiographic findings were compared with pre‐ and postcontrast thoracic CT findings. Aortic mineralization was detected using CT in 18/42 dogs (43%). Three dogs had faint diffuse aortic wall mineralization. Using CT as the reference standard, radiographs had a sensitivity and specificity of 6% and 96%, respectively, for detecting aortic mineralization. A total of 20 aortic aneurysms were detected using CT in 15/42 dogs (36%). Using CT as the reference standard, radiographs had a sensitivity and specificity of 86% and 56%, respectively, for detecting aortic aneurysms. Respiratory motion, aortic displacement by esophageal masses and Spirocerca nodules adjacent to the aorta mimicked aneurysm formation on radiographs. Aortic thrombi were seen in two dogs in postcontrast CT images. Findings from this study indicated that aortic mineralization and aneurysm formation are common in dogs with spirocercosis. Findings also supported the use of pre‐ and postcontrast CT as effective methods for detecting and characterizing these lesions.     

Progression of mycosis of the auditory tube diverticulum (guttural pouch) after arterial occlusion in a horse with contralateral temporohyoid osteoarthropathy

CASE DESCRIPTION: A 6-year-old Appaloosa mare was examined because of inappetance, difficulty eating, and swelling and mucopurulent discharge in the right eye. CLINICAL FINDINGS: Results of a CBC and serum bio-chemical analysis revealed no important findings. Ophthalmologic examination revealed scarring and ulceration of the superficial layers of the cornea. Endoscopic examination of the upper portion of the respiratory tract and auditory tube diverticula (guttural pouches) revealed abnormal thickness of the right stylohyoid bone and a plaque suggestive of mycotic growth on the left internal carotid artery. Radiographic examination revealed right-sided otitis media. Temporohyoid osteoarthropathy in the right guttural pouch and mycosis in the left guttural pouch were diagnosed. TREATMENT AND OUTCOME: Ceratohyoidectomy of the right stylohyoid bone was performed, and the left internal carotid artery was occluded via placement of stainless steel spring embolization coils. The mare regained the ability to eat without difficulty and improved clinically for approximately 4 weeks. However, the mare returned to the medical center 53 days after surgery with left-sided Horner syndrome, atrophy of the right side of the tongue, and a 3-week history of dysphagia and weight loss. Endoscopic evaluation revealed progression of mycotic growth in the left guttural pouch. The mare was euthanatized. CLINICAL RELEVANCE: Although the mycotic lesion in the left guttural pouch was an incidental finding at the time of initial examination, the lesion progressed to cause dysphagia and Horner syndrome after occlusion of the left internal carotid artery, a treatment that is typically associated with resolution of guttural pouch mycosis. Arterial occlusion is not necessarily a reliable method of resolving guttural pouch mycosis.